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<h1 id="index">Index</h1>

<div class="genindex-jumpbox">
 <a href="#A"><strong>A</strong></a>
 | <a href="#B"><strong>B</strong></a>
 | <a href="#C"><strong>C</strong></a>
 | <a href="#D"><strong>D</strong></a>
 | <a href="#E"><strong>E</strong></a>
 | <a href="#F"><strong>F</strong></a>
 | <a href="#G"><strong>G</strong></a>
 | <a href="#H"><strong>H</strong></a>
 | <a href="#I"><strong>I</strong></a>
 | <a href="#K"><strong>K</strong></a>
 | <a href="#L"><strong>L</strong></a>
 | <a href="#M"><strong>M</strong></a>
 | <a href="#N"><strong>N</strong></a>
 | <a href="#O"><strong>O</strong></a>
 | <a href="#P"><strong>P</strong></a>
 | <a href="#R"><strong>R</strong></a>
 | <a href="#S"><strong>S</strong></a>
 | <a href="#T"><strong>T</strong></a>
 | <a href="#U"><strong>U</strong></a>
 | <a href="#V"><strong>V</strong></a>
 | <a href="#W"><strong>W</strong></a>
 | <a href="#X"><strong>X</strong></a>
 | <a href="#Y"><strong>Y</strong></a>
 | <a href="#Z"><strong>Z</strong></a>
 | <a href="#Ξ"><strong>Ξ</strong></a>
 
</div>
<h2 id="A">A</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.Box.html#atomman.Box.a">a() (atomman.Box property)</a>
</li>
      <li><a href="atomman.defect.Stroh.html#atomman.defect.Stroh.A">A() (atomman.defect.Stroh property)</a>
</li>
      <li><a href="atomman.library.record.ReferenceCrystal.html#atomman.library.record.ReferenceCrystal.a">a() (atomman.library.record.ReferenceCrystal property)</a>

      <ul>
        <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.a">(atomman.library.record.RelaxedCrystal property)</a>
</li>
      </ul></li>
      <li><a href="atomman.defect.GammaSurface.html#atomman.defect.GammaSurface.a12_to_pos">a12_to_pos() (atomman.defect.GammaSurface method)</a>
</li>
      <li><a href="atomman.defect.GammaSurface.html#atomman.defect.GammaSurface.a12_to_xy">a12_to_xy() (atomman.defect.GammaSurface method)</a>
</li>
      <li><a href="atomman.defect.GammaSurface.html#atomman.defect.GammaSurface.a1vect">a1vect() (atomman.defect.GammaSurface property)</a>
</li>
      <li><a href="atomman.defect.StackingFault.html#atomman.defect.StackingFault.a1vect_cart">a1vect_cart() (atomman.defect.StackingFault property)</a>
</li>
      <li><a href="atomman.defect.StackingFault.html#atomman.defect.StackingFault.a1vect_uvw">a1vect_uvw() (atomman.defect.StackingFault property)</a>
</li>
      <li><a href="atomman.defect.GammaSurface.html#atomman.defect.GammaSurface.a2vect">a2vect() (atomman.defect.GammaSurface property)</a>
</li>
      <li><a href="atomman.defect.StackingFault.html#atomman.defect.StackingFault.a2vect_cart">a2vect_cart() (atomman.defect.StackingFault property)</a>
</li>
      <li><a href="atomman.defect.StackingFault.html#atomman.defect.StackingFault.a2vect_uvw">a2vect_uvw() (atomman.defect.StackingFault property)</a>
</li>
      <li><a href="atomman.region.html#atomman.region.Plane.above">above() (atomman.region.Plane method)</a>
</li>
      <li><a href="atomman.defect.StackingFault.html#atomman.defect.StackingFault.abovefault">abovefault() (atomman.defect.StackingFault property)</a>
</li>
      <li><a href="atomman.Box.html#atomman.Box.alpha">alpha() (atomman.Box property)</a>

      <ul>
        <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.alpha">(atomman.defect.SDVPN property)</a>
</li>
        <li><a href="atomman.library.record.ReferenceCrystal.html#atomman.library.record.ReferenceCrystal.alpha">(atomman.library.record.ReferenceCrystal property)</a>
</li>
        <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.alpha">(atomman.library.record.RelaxedCrystal property)</a>
</li>
      </ul></li>
      <li><a href="atomman.defect.Strain.html#atomman.defect.Strain.angularvelocity">angularvelocity() (atomman.defect.Strain property)</a>
</li>
      <li><a href="atomman.mep.BasePath.html#atomman.mep.BasePath.arccoord">arccoord() (atomman.mep.BasePath property)</a>
</li>
      <li><a href="atomman.defect.Dislocation.html#atomman.defect.Dislocation.array_boundary">array_boundary() (atomman.defect.Dislocation method)</a>
</li>
      <li><a href="atomman.defect.DifferentialDisplacement.html#atomman.defect.DifferentialDisplacement.arrowcenters">arrowcenters() (atomman.defect.DifferentialDisplacement property)</a>
</li>
      <li><a href="atomman.defect.DifferentialDisplacement.html#atomman.defect.DifferentialDisplacement.arrowuvectors">arrowuvectors() (atomman.defect.DifferentialDisplacement property)</a>
</li>
      <li><a href="atomman.defect.Strain.html#atomman.defect.Strain.asdict">asdict (atomman.defect.Strain attribute)</a>
</li>
      <li><a href="atomman.tools.html#atomman.tools.aslist">aslist() (in module atomman.tools)</a>
</li>
      <li><a href="atomman.tools.html#atomman.tools.atomic_mass">atomic_mass() (in module atomman.tools)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.tools.html#atomman.tools.atomic_number">atomic_number() (in module atomman.tools)</a>
</li>
      <li><a href="atomman.tools.html#atomman.tools.atomic_symbol">atomic_symbol() (in module atomman.tools)</a>
</li>
      <li><a href="atomman.html#module-atomman">atomman (module)</a>
</li>
      <li><a href="atomman.defect.html#module-atomman.defect">atomman.defect (module)</a>
</li>
      <li><a href="atomman.lammps.html#module-atomman.lammps">atomman.lammps (module)</a>
</li>
      <li><a href="atomman.lammps.html#module-atomman.lammps.Potential">atomman.lammps.Potential (module)</a>
</li>
      <li><a href="atomman.lammps.html#module-atomman.lammps.style">atomman.lammps.style (module)</a>
</li>
      <li><a href="atomman.mep.html#module-atomman.mep">atomman.mep (module)</a>
</li>
      <li><a href="atomman.mep.html#module-atomman.mep.gradient">atomman.mep.gradient (module)</a>
</li>
      <li><a href="atomman.mep.html#module-atomman.mep.integrator">atomman.mep.integrator (module)</a>
</li>
      <li><a href="atomman.plot.html#module-atomman.plot">atomman.plot (module)</a>
</li>
      <li><a href="atomman.region.html#module-atomman.region">atomman.region (module)</a>
</li>
      <li><a href="atomman.tools.html#module-atomman.tools">atomman.tools (module)</a>
</li>
      <li><a href="atomman.tools.html#module-atomman.tools.miller">atomman.tools.miller (module)</a>
</li>
      <li><a href="atomman.unitconvert.html#module-atomman.unitconvert">atomman.unitconvert (module)</a>
</li>
      <li><a href="atomman.Atoms.html#atomman.Atoms">Atoms (class in atomman)</a>
</li>
      <li><a href="atomman.System.html#atomman.System.atoms">atoms() (atomman.System property)</a>
</li>
      <li><a href="atomman.Atoms.html#atomman.Atoms.PropertyDict">Atoms.PropertyDict (class in atomman)</a>
</li>
      <li><a href="atomman.System.html#atomman.System.atoms_df">atoms_df() (atomman.System method)</a>
</li>
      <li><a href="atomman.System.html#atomman.System.atoms_extend">atoms_extend() (atomman.System method)</a>
</li>
      <li><a href="atomman.System.html#atomman.System.atoms_ix">atoms_ix() (atomman.System property)</a>
</li>
      <li><a href="atomman.System.html#atomman.System.atoms_prop">atoms_prop() (atomman.System method)</a>
</li>
      <li><a href="atomman.Atoms.html#atomman.Atoms.atypes">atypes() (atomman.Atoms property)</a>

      <ul>
        <li><a href="atomman.System.html#atomman.System.atypes">(atomman.System property)</a>
</li>
      </ul></li>
      <li><a href="atomman.Box.html#atomman.Box.avect">avect() (atomman.Box property)</a>
</li>
      <li><a href="atomman.tools.html#atomman.tools.axes_check">axes_check() (in module atomman.tools)</a>
</li>
      <li><a href="atomman.region.html#atomman.region.Cylinder.axis">axis() (atomman.region.Cylinder property)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="B">B</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.Box.html#atomman.Box.b">b() (atomman.Box property)</a>

      <ul>
        <li><a href="atomman.library.record.ReferenceCrystal.html#atomman.library.record.ReferenceCrystal.b">(atomman.library.record.ReferenceCrystal property)</a>
</li>
        <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.b">(atomman.library.record.RelaxedCrystal property)</a>
</li>
      </ul></li>
      <li><a href="atomman.defect.Dislocation.html#atomman.defect.Dislocation.base_system">base_system() (atomman.defect.Dislocation property)</a>
</li>
      <li><a href="atomman.mep.BasePath.html#atomman.mep.BasePath">BasePath (class in atomman.mep)</a>
</li>
      <li><a href="atomman.region.html#atomman.region.Plane.below">below() (atomman.region.Plane method)</a>
</li>
      <li><a href="atomman.Box.html#atomman.Box.beta">beta() (atomman.Box property)</a>

      <ul>
        <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.beta">(atomman.defect.SDVPN property)</a>
</li>
        <li><a href="atomman.library.record.ReferenceCrystal.html#atomman.library.record.ReferenceCrystal.beta">(atomman.library.record.ReferenceCrystal property)</a>
</li>
        <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.beta">(atomman.library.record.RelaxedCrystal property)</a>
</li>
      </ul></li>
      <li><a href="atomman.cluster.BondAngleMap.html#atomman.cluster.BondAngleMap">BondAngleMap (class in atomman.cluster)</a>
</li>
      <li><a href="atomman.Box.html#atomman.Box">Box (class in atomman)</a>
</li>
      <li><a href="atomman.defect.GammaSurface.html#atomman.defect.GammaSurface.box">box() (atomman.defect.GammaSurface property)</a>

      <ul>
        <li><a href="atomman.System.html#atomman.System.box">(atomman.System property)</a>
</li>
      </ul></li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.defect.Dislocation.html#atomman.defect.Dislocation.box_boundary">box_boundary() (atomman.defect.Dislocation method)</a>
</li>
      <li><a href="atomman.System.html#atomman.System.box_set">box_set() (atomman.System method)</a>
</li>
      <li><a href="atomman.NeighborList.html#atomman.NeighborList.build">build() (atomman.NeighborList method)</a>
</li>
      <li><a href="atomman.html#atomman.build_lammps_potential">build_lammps_potential() (in module atomman)</a>
</li>
      <li><a href="atomman.library.record.CrystalPrototype.html#atomman.library.record.CrystalPrototype.build_model">build_model() (atomman.library.record.CrystalPrototype method)</a>

      <ul>
        <li><a href="atomman.library.record.ReferenceCrystal.html#atomman.library.record.ReferenceCrystal.build_model">(atomman.library.record.ReferenceCrystal method)</a>
</li>
        <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.build_model">(atomman.library.record.RelaxedCrystal method)</a>
</li>
      </ul></li>
      <li><a href="atomman.defect.Strain.html#atomman.defect.Strain.build_p_vectors">build_p_vectors (atomman.defect.Strain attribute)</a>
</li>
      <li><a href="atomman.defect.GammaSurface.html#atomman.defect.GammaSurface.build_path">build_path() (atomman.defect.GammaSurface method)</a>
</li>
      <li><a href="atomman.unitconvert.html#atomman.unitconvert.build_unit">build_unit() (in module atomman.unitconvert)</a>
</li>
      <li><a href="atomman.ElasticConstants.html#atomman.ElasticConstants.bulk">bulk() (atomman.ElasticConstants method)</a>
</li>
      <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.burgers">burgers() (atomman.defect.SDVPN property)</a>

      <ul>
        <li><a href="atomman.defect.VolterraDislocation.html#atomman.defect.VolterraDislocation.burgers">(atomman.defect.VolterraDislocation property)</a>
</li>
      </ul></li>
      <li><a href="atomman.Box.html#atomman.Box.bvect">bvect() (atomman.Box property)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="C">C</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.Box.html#atomman.Box.c">c() (atomman.Box property)</a>
</li>
      <li><a href="atomman.defect.VolterraDislocation.html#atomman.defect.VolterraDislocation.C">C() (atomman.defect.VolterraDislocation property)</a>
</li>
      <li><a href="atomman.library.record.ReferenceCrystal.html#atomman.library.record.ReferenceCrystal.c">c() (atomman.library.record.ReferenceCrystal property)</a>

      <ul>
        <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.c">(atomman.library.record.RelaxedCrystal property)</a>
</li>
      </ul></li>
      <li><a href="atomman.library.record.CrystalPrototype.html#atomman.library.record.CrystalPrototype.cdcsquery">cdcsquery() (atomman.library.record.CrystalPrototype static method)</a>

      <ul>
        <li><a href="atomman.library.record.ReferenceCrystal.html#atomman.library.record.ReferenceCrystal.cdcsquery">(atomman.library.record.ReferenceCrystal static method)</a>
</li>
        <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.cdcsquery">(atomman.library.record.RelaxedCrystal static method)</a>
</li>
      </ul></li>
      <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.cdiffelastic">cdiffelastic() (atomman.defect.SDVPN property)</a>
</li>
      <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.cdiffstress">cdiffstress() (atomman.defect.SDVPN property)</a>
</li>
      <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.cdiffsurface">cdiffsurface() (atomman.defect.SDVPN property)</a>
</li>
      <li><a href="atomman.region.html#atomman.region.Sphere.center">center() (atomman.region.Sphere property)</a>
</li>
      <li><a href="atomman.region.html#atomman.region.Cylinder.center1">center1() (atomman.region.Cylinder property)</a>
</li>
      <li><a href="atomman.region.html#atomman.region.Cylinder.center2">center2() (atomman.region.Cylinder property)</a>
</li>
      <li><a href="atomman.mep.html#atomman.mep.gradient.central_difference">central_difference() (in module atomman.mep.gradient)</a>
</li>
      <li><a href="atomman.defect.VolterraDislocation.html#atomman.defect.VolterraDislocation.characterangle">characterangle() (atomman.defect.VolterraDislocation method)</a>
</li>
      <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.check_energies">check_energies() (atomman.defect.SDVPN method)</a>
</li>
      <li><a href="atomman.lammps.html#atomman.lammps.checkversion">checkversion() (in module atomman.lammps)</a>
</li>
      <li><a href="atomman.ElasticConstants.html#atomman.ElasticConstants.Cij">Cij() (atomman.ElasticConstants property)</a>
</li>
      <li><a href="atomman.ElasticConstants.html#atomman.ElasticConstants.Cij9">Cij9() (atomman.ElasticConstants property)</a>
</li>
      <li><a href="atomman.ElasticConstants.html#atomman.ElasticConstants.Cijkl">Cijkl() (atomman.ElasticConstants property)</a>
</li>
      <li><a href="atomman.defect.Strain.html#atomman.defect.Strain.clear_properties">clear_properties (atomman.defect.Strain attribute)</a>
</li>
      <li><a href="atomman.lammps.NEBLog.html#atomman.lammps.NEBLog.climbrun">climbrun() (atomman.lammps.NEBLog property)</a>
</li>
      <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.cohesive_energy">cohesive_energy() (atomman.library.record.RelaxedCrystal property)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.library.record.CrystalPrototype.html#atomman.library.record.CrystalPrototype.commonname">commonname() (atomman.library.record.CrystalPrototype property)</a>
</li>
      <li><a href="atomman.library.record.ReferenceCrystal.html#atomman.library.record.ReferenceCrystal.composition">composition() (atomman.library.record.ReferenceCrystal property)</a>

      <ul>
        <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.composition">(atomman.library.record.RelaxedCrystal property)</a>
</li>
        <li><a href="atomman.System.html#atomman.System.composition">(atomman.System property)</a>
</li>
      </ul></li>
      <li><a href="atomman.tools.html#atomman.tools.compositionstr">compositionstr() (in module atomman.tools)</a>
</li>
      <li><a href="atomman.defect.FreeSurface.html#atomman.defect.FreeSurface.conventional_setting">conventional_setting() (atomman.defect.FreeSurface property)</a>
</li>
      <li><a href="atomman.mep.BasePath.html#atomman.mep.BasePath.coord">coord() (atomman.mep.BasePath property)</a>

      <ul>
        <li><a href="atomman.NeighborList.html#atomman.NeighborList.coord">(atomman.NeighborList property)</a>
</li>
      </ul></li>
      <li><a href="atomman.mep.html#atomman.mep.create_path">create_path() (in module atomman.mep)</a>
</li>
      <li><a href="atomman.library.record.CrystalPrototype.html#atomman.library.record.CrystalPrototype.crystalfamily">crystalfamily() (atomman.library.record.CrystalPrototype property)</a>

      <ul>
        <li><a href="atomman.library.record.ReferenceCrystal.html#atomman.library.record.ReferenceCrystal.crystalfamily">(atomman.library.record.ReferenceCrystal property)</a>
</li>
        <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.crystalfamily">(atomman.library.record.RelaxedCrystal property)</a>
</li>
      </ul></li>
      <li><a href="atomman.library.record.CrystalPrototype.html#atomman.library.record.CrystalPrototype">CrystalPrototype (class in atomman.library.record)</a>
</li>
      <li><a href="atomman.Box.html#atomman.Box.cubic">cubic() (atomman.Box class method)</a>

      <ul>
        <li><a href="atomman.ElasticConstants.html#atomman.ElasticConstants.cubic">(atomman.ElasticConstants method)</a>
</li>
      </ul></li>
      <li><a href="atomman.cluster.BondAngleMap.html#atomman.cluster.BondAngleMap.cumulative_pdf">cumulative_pdf() (atomman.cluster.BondAngleMap method)</a>
</li>
      <li><a href="atomman.defect.FreeSurface.html#atomman.defect.FreeSurface.cutboxvector">cutboxvector() (atomman.defect.FreeSurface property)</a>
</li>
      <li><a href="atomman.defect.Dislocation.html#atomman.defect.Dislocation.cutindex">cutindex() (atomman.defect.Dislocation property)</a>

      <ul>
        <li><a href="atomman.defect.FreeSurface.html#atomman.defect.FreeSurface.cutindex">(atomman.defect.FreeSurface property)</a>
</li>
      </ul></li>
      <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.cutofflongrange">cutofflongrange() (atomman.defect.SDVPN property)</a>
</li>
      <li><a href="atomman.Box.html#atomman.Box.cvect">cvect() (atomman.Box property)</a>
</li>
      <li><a href="atomman.region.html#atomman.region.Cylinder">Cylinder (class in atomman.region)</a>
</li>
      <li><a href="atomman.defect.Dislocation.html#atomman.defect.Dislocation.cylinder_boundary">cylinder_boundary() (atomman.defect.Dislocation method)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="D">D</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.defect.GammaSurface.html#atomman.defect.GammaSurface.data">data() (atomman.defect.GammaSurface property)</a>
</li>
      <li><a href="atomman.library.Database.html#atomman.library.Database">Database (class in atomman.library)</a>
</li>
      <li><a href="atomman.defect.DifferentialDisplacement.html#atomman.defect.DifferentialDisplacement.ddvectors">ddvectors() (atomman.defect.DifferentialDisplacement property)</a>
</li>
      <li><a href="atomman.mep.ISMPath.html#atomman.mep.ISMPath.default_timestep">default_timestep() (atomman.mep.ISMPath property)</a>
</li>
      <li><a href="atomman.mep.ISMPath.html#atomman.mep.ISMPath.default_tolerance">default_tolerance() (atomman.mep.ISMPath property)</a>
</li>
      <li><a href="atomman.defect.GammaSurface.html#atomman.defect.GammaSurface.delta">delta() (atomman.defect.GammaSurface method)</a>
</li>
      <li><a href="atomman.defect.GammaSurface.html#atomman.defect.GammaSurface.delta_line_plot">delta_line_plot() (atomman.defect.GammaSurface method)</a>
</li>
      <li><a href="atomman.defect.GammaSurface.html#atomman.defect.GammaSurface.delta_surface_plot">delta_surface_plot() (atomman.defect.GammaSurface method)</a>
</li>
      <li><a href="atomman.Atoms.html#atomman.Atoms.df">df() (atomman.Atoms method)</a>

      <ul>
        <li><a href="atomman.cluster.BondAngleMap.html#atomman.cluster.BondAngleMap.df">(atomman.cluster.BondAngleMap property)</a>
</li>
      </ul></li>
      <li><a href="atomman.defect.html#atomman.defect.differential_displacement">differential_displacement() (in module atomman.defect)</a>
</li>
      <li><a href="atomman.defect.DifferentialDisplacement.html#atomman.defect.DifferentialDisplacement">DifferentialDisplacement (class in atomman.defect)</a>
</li>
      <li><a href="atomman.defect.Dislocation.html#atomman.defect.Dislocation.disl_system">disl_system() (atomman.defect.Dislocation property)</a>
</li>
      <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.disldensity">disldensity() (atomman.defect.SDVPN method)</a>
</li>
      <li><a href="atomman.defect.Dislocation.html#atomman.defect.Dislocation">Dislocation (class in atomman.defect)</a>
</li>
      <li><a href="atomman.defect.html#atomman.defect.dislocation_array">dislocation_array() (in module atomman.defect)</a>
</li>
      <li><a href="atomman.defect.html#atomman.defect.dislocation_system_transform">dislocation_system_transform() (in module atomman.defect)</a>
</li>
      <li><a href="atomman.defect.Dislocation.html#atomman.defect.Dislocation.dislsol">dislsol() (atomman.defect.Dislocation property)</a>
</li>
      <li><a href="atomman.defect.IsotropicVolterraDislocation.html#atomman.defect.IsotropicVolterraDislocation.displacement">displacement() (atomman.defect.IsotropicVolterraDislocation method)</a>

      <ul>
        <li><a href="atomman.defect.Stroh.html#atomman.defect.Stroh.displacement">(atomman.defect.Stroh method)</a>
</li>
        <li><a href="atomman.defect.VolterraDislocation.html#atomman.defect.VolterraDislocation.displacement">(atomman.defect.VolterraDislocation method)</a>
</li>
        <li><a href="atomman.html#atomman.displacement">(in module atomman)</a>
</li>
      </ul></li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.disregistry">disregistry() (atomman.defect.SDVPN property)</a>

      <ul>
        <li><a href="atomman.defect.html#atomman.defect.disregistry">(in module atomman.defect)</a>
</li>
      </ul></li>
      <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.disregistry_plot">disregistry_plot() (atomman.defect.SDVPN method)</a>
</li>
      <li><a href="atomman.System.html#atomman.System.dmag">dmag() (atomman.System method)</a>

      <ul>
        <li><a href="atomman.html#atomman.dmag">(in module atomman)</a>
</li>
      </ul></li>
      <li><a href="atomman.library.Database.html#atomman.library.Database.download_all">download_all() (atomman.library.Database method)</a>
</li>
      <li><a href="atomman.library.Database.html#atomman.library.Database.download_crystal_prototypes">download_crystal_prototypes() (atomman.library.Database method)</a>
</li>
      <li><a href="atomman.library.Database.html#atomman.library.Database.download_reference_crystals">download_reference_crystals() (atomman.library.Database method)</a>
</li>
      <li><a href="atomman.library.Database.html#atomman.library.Database.download_relaxed_crystals">download_relaxed_crystals() (atomman.library.Database method)</a>
</li>
      <li><a href="atomman.defect.html#atomman.defect.dumbbell">dumbbell() (in module atomman.defect)</a>
</li>
      <li><a href="atomman.NeighborList.html#atomman.NeighborList.dump">dump() (atomman.NeighborList method)</a>

      <ul>
        <li><a href="atomman.System.html#atomman.System.dump">(atomman.System method)</a>
</li>
        <li><a href="atomman.html#atomman.dump">(in module atomman)</a>
</li>
      </ul></li>
      <li><a href="atomman.html#atomman.dump_ase_Atoms">dump_ase_Atoms() (in module atomman)</a>
</li>
      <li><a href="atomman.html#atomman.dump_atom_data">dump_atom_data() (in module atomman)</a>
</li>
      <li><a href="atomman.html#atomman.dump_atom_dump">dump_atom_dump() (in module atomman)</a>
</li>
      <li><a href="atomman.html#atomman.dump_poscar">dump_poscar() (in module atomman)</a>
</li>
      <li><a href="atomman.html#atomman.dump_pymatgen_Structure">dump_pymatgen_Structure() (in module atomman)</a>
</li>
      <li><a href="atomman.html#atomman.dump_system_model">dump_system_model() (in module atomman)</a>
</li>
      <li><a href="atomman.html#atomman.dump_table">dump_table() (in module atomman)</a>
</li>
      <li><a href="atomman.tools.html#atomman.tools.duplicates_allclose">duplicates_allclose (in module atomman.tools)</a>
</li>
      <li><a href="atomman.System.html#atomman.System.dvect">dvect() (atomman.System method)</a>

      <ul>
        <li><a href="atomman.html#atomman.dvect">(in module atomman)</a>
</li>
      </ul></li>
  </ul></td>
</tr></table>

<h2 id="E">E</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.defect.GammaSurface.html#atomman.defect.GammaSurface.E_gsf">E_gsf() (atomman.defect.GammaSurface method)</a>
</li>
      <li><a href="atomman.defect.GammaSurface.html#atomman.defect.GammaSurface.E_gsf_line_plot">E_gsf_line_plot() (atomman.defect.GammaSurface method)</a>
</li>
      <li><a href="atomman.defect.GammaSurface.html#atomman.defect.GammaSurface.E_gsf_surface_plot">E_gsf_surface_plot() (atomman.defect.GammaSurface method)</a>

      <ul>
        <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.E_gsf_surface_plot">(atomman.defect.SDVPN method)</a>
</li>
      </ul></li>
      <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.E_gsf_vs_x_plot">E_gsf_vs_x_plot() (atomman.defect.SDVPN method)</a>
</li>
      <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.elastic_energy">elastic_energy() (atomman.defect.SDVPN method)</a>
</li>
      <li><a href="atomman.ElasticConstants.html#atomman.ElasticConstants">ElasticConstants (class in atomman)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.region.html#atomman.region.Cylinder.endcaps">endcaps() (atomman.region.Cylinder property)</a>
</li>
      <li><a href="atomman.mep.BasePath.html#atomman.mep.BasePath.energy">energy() (atomman.mep.BasePath method)</a>
</li>
      <li><a href="atomman.mep.BasePath.html#atomman.mep.BasePath.energyfxn">energyfxn() (atomman.mep.BasePath property)</a>
</li>
      <li><a href="atomman.unitconvert.html#atomman.unitconvert.error_unit">error_unit() (in module atomman.unitconvert)</a>
</li>
      <li><a href="atomman.defect.Stroh.html#atomman.defect.Stroh.eta">eta() (atomman.defect.Stroh method)</a>
</li>
      <li><a href="atomman.mep.html#atomman.mep.integrator.euler">euler() (in module atomman.mep.integrator)</a>
</li>
      <li><a href="atomman.Atoms.html#atomman.Atoms.extend">extend() (atomman.Atoms method)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="F">F</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.family">family() (atomman.library.record.RelaxedCrystal property)</a>
</li>
      <li><a href="atomman.defect.StackingFault.html#atomman.defect.StackingFault.fault">fault() (atomman.defect.StackingFault method)</a>
</li>
      <li><a href="atomman.defect.StackingFault.html#atomman.defect.StackingFault.faultpos_cart">faultpos_cart() (atomman.defect.StackingFault property)</a>
</li>
      <li><a href="atomman.defect.StackingFault.html#atomman.defect.StackingFault.faultpos_rel">faultpos_rel() (atomman.defect.StackingFault property)</a>
</li>
      <li><a href="atomman.library.Database.html#atomman.library.Database.fetch_mp_crystal">fetch_mp_crystal() (atomman.library.Database method)</a>
</li>
      <li><a href="atomman.library.Database.html#atomman.library.Database.fetch_mp_crystals">fetch_mp_crystals() (atomman.library.Database method)</a>
</li>
      <li><a href="atomman.library.Database.html#atomman.library.Database.fetch_oqmd_crystal">fetch_oqmd_crystal() (atomman.library.Database method)</a>
</li>
      <li><a href="atomman.library.Database.html#atomman.library.Database.fetch_reference_crystal">fetch_reference_crystal() (atomman.library.Database method)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.tools.html#atomman.tools.filltemplate">filltemplate() (in module atomman.tools)</a>
</li>
      <li><a href="atomman.defect.GammaSurface.html#atomman.defect.GammaSurface.fit">fit() (atomman.defect.GammaSurface method)</a>
</li>
      <li><a href="atomman.lammps.Log.html#atomman.lammps.Log.flatten">flatten() (atomman.lammps.Log method)</a>
</li>
      <li><a href="atomman.mep.BasePath.html#atomman.mep.BasePath.force">force() (atomman.mep.BasePath property)</a>
</li>
      <li><a href="atomman.defect.html#atomman.defect.free_surface_basis">free_surface_basis() (in module atomman.defect)</a>
</li>
      <li><a href="atomman.defect.FreeSurface.html#atomman.defect.FreeSurface">FreeSurface (class in atomman.defect)</a>
</li>
      <li><a href="atomman.defect.Dislocation.html#atomman.defect.Dislocation.fromref">fromref() (atomman.defect.Dislocation class method)</a>
</li>
      <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.fullstress">fullstress() (atomman.defect.SDVPN property)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="G">G</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.defect.Strain.html#atomman.defect.Strain.G">G() (atomman.defect.Strain property)</a>
</li>
      <li><a href="atomman.Box.html#atomman.Box.gamma">gamma() (atomman.Box property)</a>

      <ul>
        <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.gamma">(atomman.defect.SDVPN property)</a>
</li>
        <li><a href="atomman.library.record.ReferenceCrystal.html#atomman.library.record.ReferenceCrystal.gamma">(atomman.library.record.ReferenceCrystal property)</a>
</li>
        <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.gamma">(atomman.library.record.RelaxedCrystal property)</a>
</li>
      </ul></li>
      <li><a href="atomman.defect.GammaSurface.html#atomman.defect.GammaSurface">GammaSurface (class in atomman.defect)</a>
</li>
      <li><a href="atomman.lammps.NEBLog.html#atomman.lammps.NEBLog.get_barrier">get_barrier() (atomman.lammps.NEBLog method)</a>
</li>
      <li><a href="atomman.library.Database.html#atomman.library.Database.get_crystal_prototype">get_crystal_prototype() (atomman.library.Database method)</a>
</li>
      <li><a href="atomman.library.Database.html#atomman.library.Database.get_crystal_prototypes">get_crystal_prototypes() (atomman.library.Database method)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.unitconvert.html#atomman.unitconvert.get_in_units">get_in_units() (in module atomman.unitconvert)</a>
</li>
      <li><a href="atomman.lammps.NEBLog.html#atomman.lammps.NEBLog.get_neb_path">get_neb_path() (atomman.lammps.NEBLog method)</a>
</li>
      <li><a href="atomman.library.Database.html#atomman.library.Database.get_reference_crystal">get_reference_crystal() (atomman.library.Database method)</a>
</li>
      <li><a href="atomman.library.Database.html#atomman.library.Database.get_reference_crystals">get_reference_crystals() (atomman.library.Database method)</a>
</li>
      <li><a href="atomman.library.Database.html#atomman.library.Database.get_relaxed_crystal">get_relaxed_crystal() (atomman.library.Database method)</a>
</li>
      <li><a href="atomman.library.Database.html#atomman.library.Database.get_relaxed_crystals">get_relaxed_crystals() (atomman.library.Database method)</a>
</li>
      <li><a href="atomman.mep.BasePath.html#atomman.mep.BasePath.grad_energy">grad_energy() (atomman.mep.BasePath method)</a>
</li>
      <li><a href="atomman.mep.BasePath.html#atomman.mep.BasePath.gradientfxn">gradientfxn() (atomman.mep.BasePath property)</a>
</li>
      <li><a href="atomman.mep.BasePath.html#atomman.mep.BasePath.gradientkwargs">gradientkwargs() (atomman.mep.BasePath property)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="H">H</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.Box.html#atomman.Box.hexagonal">hexagonal() (atomman.Box class method)</a>

      <ul>
        <li><a href="atomman.ElasticConstants.html#atomman.ElasticConstants.hexagonal">(atomman.ElasticConstants method)</a>
</li>
      </ul></li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.defect.FreeSurface.html#atomman.defect.FreeSurface.hkl">hkl() (atomman.defect.FreeSurface property)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="I">I</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.tools.html#atomman.tools.iaslist">iaslist() (in module atomman.tools)</a>
</li>
      <li><a href="atomman.library.record.CrystalPrototype.html#atomman.library.record.CrystalPrototype.id">id() (atomman.library.record.CrystalPrototype property)</a>

      <ul>
        <li><a href="atomman.library.record.ReferenceCrystal.html#atomman.library.record.ReferenceCrystal.id">(atomman.library.record.ReferenceCrystal property)</a>
</li>
      </ul></li>
      <li><a href="atomman.tools.html#atomman.tools.identifyfamily">identifyfamily() (in module atomman.tools)</a>
</li>
      <li><a href="atomman.tools.html#atomman.tools.indexstr">indexstr() (in module atomman.tools)</a>
</li>
      <li><a href="atomman.Box.html#atomman.Box.inside">inside() (atomman.Box method)</a>

      <ul>
        <li><a href="atomman.region.html#atomman.region.Cylinder.inside">(atomman.region.Cylinder method)</a>
</li>
        <li><a href="atomman.region.html#atomman.region.PlaneSet.inside">(atomman.region.PlaneSet method)</a>
</li>
        <li><a href="atomman.region.html#atomman.region.Shape.inside">(atomman.region.Shape method)</a>
</li>
        <li><a href="atomman.region.html#atomman.region.Sphere.inside">(atomman.region.Sphere method)</a>
</li>
      </ul></li>
      <li><a href="atomman.mep.BasePath.html#atomman.mep.BasePath.integratorfxn">integratorfxn() (atomman.mep.BasePath property)</a>
</li>
      <li><a href="atomman.plot.html#atomman.plot.interpolate_contour">interpolate_contour() (in module atomman.plot)</a>
</li>
      <li><a href="atomman.mep.ISMPath.html#atomman.mep.ISMPath.interpolate_path">interpolate_path() (atomman.mep.ISMPath method)</a>
</li>
      <li><a href="atomman.defect.html#atomman.defect.interstitial">interstitial() (in module atomman.defect)</a>
</li>
      <li><a href="atomman.defect.Strain.html#atomman.defect.Strain.invariant1">invariant1() (atomman.defect.Strain property)</a>
</li>
      <li><a href="atomman.defect.Strain.html#atomman.defect.Strain.invariant2">invariant2() (atomman.defect.Strain property)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.defect.Strain.html#atomman.defect.Strain.invariant3">invariant3() (atomman.defect.Strain property)</a>
</li>
      <li><a href="atomman.Box.html#atomman.Box.is_lammps_norm">is_lammps_norm() (atomman.Box method)</a>
</li>
      <li><a href="atomman.ElasticConstants.html#atomman.ElasticConstants.is_normal">is_normal() (atomman.ElasticConstants method)</a>
</li>
      <li><a href="atomman.tools.html#atomman.tools.iscubic">iscubic() (in module atomman.tools)</a>
</li>
      <li><a href="atomman.tools.html#atomman.tools.ishexagonal">ishexagonal() (in module atomman.tools)</a>
</li>
      <li><a href="atomman.tools.html#atomman.tools.ismonoclinic">ismonoclinic() (in module atomman.tools)</a>
</li>
      <li><a href="atomman.mep.ISMPath.html#atomman.mep.ISMPath">ISMPath (class in atomman.mep)</a>
</li>
      <li><a href="atomman.tools.html#atomman.tools.isorthorhombic">isorthorhombic() (in module atomman.tools)</a>
</li>
      <li><a href="atomman.ElasticConstants.html#atomman.ElasticConstants.isotropic">isotropic() (atomman.ElasticConstants method)</a>
</li>
      <li><a href="atomman.defect.IsotropicVolterraDislocation.html#atomman.defect.IsotropicVolterraDislocation">IsotropicVolterraDislocation (class in atomman.defect)</a>
</li>
      <li><a href="atomman.tools.html#atomman.tools.isrhombohedral">isrhombohedral() (in module atomman.tools)</a>
</li>
      <li><a href="atomman.tools.html#atomman.tools.istetragonal">istetragonal() (in module atomman.tools)</a>
</li>
      <li><a href="atomman.tools.html#atomman.tools.istriclinic">istriclinic() (in module atomman.tools)</a>
</li>
      <li><a href="atomman.cluster.BondAngleMap.html#atomman.cluster.BondAngleMap.itercoords">itercoords() (atomman.cluster.BondAngleMap method)</a>
</li>
      <li><a href="atomman.defect.StackingFault.html#atomman.defect.StackingFault.iterfaultmap">iterfaultmap() (atomman.defect.StackingFault method)</a>
</li>
      <li><a href="atomman.cluster.BondAngleMap.html#atomman.cluster.BondAngleMap.itersystem">itersystem() (atomman.cluster.BondAngleMap method)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="K">K</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.defect.Stroh.html#atomman.defect.Stroh.k">k() (atomman.defect.Stroh property)</a>
</li>
      <li><a href="atomman.defect.Stroh.html#atomman.defect.Stroh.K_coeff">K_coeff() (atomman.defect.Stroh property)</a>

      <ul>
        <li><a href="atomman.defect.VolterraDislocation.html#atomman.defect.VolterraDislocation.K_coeff">(atomman.defect.VolterraDislocation property)</a>
</li>
      </ul></li>
      <li><a href="atomman.defect.IsotropicVolterraDislocation.html#atomman.defect.IsotropicVolterraDislocation.K_tensor">K_tensor() (atomman.defect.IsotropicVolterraDislocation property)</a>

      <ul>
        <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.K_tensor">(atomman.defect.SDVPN property)</a>
</li>
        <li><a href="atomman.defect.Stroh.html#atomman.defect.Stroh.K_tensor">(atomman.defect.Stroh property)</a>
</li>
        <li><a href="atomman.defect.VolterraDislocation.html#atomman.defect.VolterraDislocation.K_tensor">(atomman.defect.VolterraDislocation property)</a>
</li>
      </ul></li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.library.record.CrystalPrototype.html#atomman.library.record.CrystalPrototype.key">key() (atomman.library.record.CrystalPrototype property)</a>

      <ul>
        <li><a href="atomman.library.record.ReferenceCrystal.html#atomman.library.record.ReferenceCrystal.key">(atomman.library.record.ReferenceCrystal property)</a>
</li>
        <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.key">(atomman.library.record.RelaxedCrystal property)</a>
</li>
      </ul></li>
  </ul></td>
</tr></table>

<h2 id="L">L</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.defect.Stroh.html#atomman.defect.Stroh.L">L() (atomman.defect.Stroh property)</a>
</li>
      <li><a href="atomman.lammps.Log.html#atomman.lammps.Log.lammps_date">lammps_date() (atomman.lammps.Log property)</a>
</li>
      <li><a href="atomman.lammps.Log.html#atomman.lammps.Log.lammps_version">lammps_version() (atomman.lammps.Log property)</a>
</li>
      <li><a href="atomman.lammps.LammpsError.html#atomman.lammps.LammpsError">LammpsError (class in atomman.lammps)</a>
</li>
      <li><a href="atomman.defect.Dislocation.html#atomman.defect.Dislocation.lineindex">lineindex() (atomman.defect.Dislocation property)</a>
</li>
      <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.load">load() (atomman.defect.SDVPN method)</a>

      <ul>
        <li><a href="atomman.lammps.NEBLog.html#atomman.lammps.NEBLog.load">(atomman.lammps.NEBLog method)</a>
</li>
        <li><a href="atomman.NeighborList.html#atomman.NeighborList.load">(atomman.NeighborList method)</a>
</li>
        <li><a href="atomman.html#atomman.load">(in module atomman)</a>
</li>
      </ul></li>
      <li><a href="atomman.html#atomman.load_ase_Atoms">load_ase_Atoms() (in module atomman)</a>
</li>
      <li><a href="atomman.html#atomman.load_atom_data">load_atom_data() (in module atomman)</a>
</li>
      <li><a href="atomman.html#atomman.load_atom_dump">load_atom_dump() (in module atomman)</a>
</li>
      <li><a href="atomman.html#atomman.load_cif">load_cif() (in module atomman)</a>
</li>
      <li><a href="atomman.html#atomman.load_crystal">load_crystal() (in module atomman)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.html#atomman.load_lammps_potential">load_lammps_potential() (in module atomman)</a>
</li>
      <li><a href="atomman.library.record.CrystalPrototype.html#atomman.library.record.CrystalPrototype.load_model">load_model() (atomman.library.record.CrystalPrototype method)</a>

      <ul>
        <li><a href="atomman.library.record.ReferenceCrystal.html#atomman.library.record.ReferenceCrystal.load_model">(atomman.library.record.ReferenceCrystal method)</a>
</li>
        <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.load_model">(atomman.library.record.RelaxedCrystal method)</a>
</li>
      </ul></li>
      <li><a href="atomman.html#atomman.load_poscar">load_poscar() (in module atomman)</a>
</li>
      <li><a href="atomman.html#atomman.load_prototype">load_prototype() (in module atomman)</a>
</li>
      <li><a href="atomman.html#atomman.load_pymatgen_Structure">load_pymatgen_Structure() (in module atomman)</a>
</li>
      <li><a href="atomman.html#atomman.load_system_model">load_system_model() (in module atomman)</a>
</li>
      <li><a href="atomman.html#atomman.load_table">load_table() (in module atomman)</a>
</li>
      <li><a href="atomman.lammps.Log.html#atomman.lammps.Log">Log (class in atomman.lammps)</a>
</li>
      <li><a href="atomman.lammps.NEBLog.html#atomman.lammps.NEBLog.logs">logs() (atomman.lammps.NEBLog property)</a>
</li>
      <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.longrange_energy">longrange_energy() (atomman.defect.SDVPN method)</a>
</li>
      <li><a href="atomman.Box.html#atomman.Box.lx">lx() (atomman.Box property)</a>
</li>
      <li><a href="atomman.Box.html#atomman.Box.ly">ly() (atomman.Box property)</a>
</li>
      <li><a href="atomman.Box.html#atomman.Box.lz">lz() (atomman.Box property)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="M">M</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.defect.VolterraDislocation.html#atomman.defect.VolterraDislocation.m">m() (atomman.defect.VolterraDislocation property)</a>
</li>
      <li><a href="atomman.System.html#atomman.System.masses">masses() (atomman.System property)</a>
</li>
      <li><a href="atomman.library.record.CrystalPrototype.html#atomman.library.record.CrystalPrototype.metadata">metadata() (atomman.library.record.CrystalPrototype method)</a>

      <ul>
        <li><a href="atomman.library.record.ReferenceCrystal.html#atomman.library.record.ReferenceCrystal.metadata">(atomman.library.record.ReferenceCrystal method)</a>
</li>
        <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.metadata">(atomman.library.record.RelaxedCrystal method)</a>
</li>
      </ul></li>
      <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.method">method() (atomman.library.record.RelaxedCrystal property)</a>
</li>
      <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.min_kwargs">min_kwargs() (atomman.defect.SDVPN property)</a>
</li>
      <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.min_method">min_method() (atomman.defect.SDVPN property)</a>
</li>
      <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.min_options">min_options() (atomman.defect.SDVPN property)</a>
</li>
      <li><a href="atomman.lammps.NEBLog.html#atomman.lammps.NEBLog.minrun">minrun() (atomman.lammps.NEBLog property)</a>
</li>
      <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.misfit_energy">misfit_energy() (atomman.defect.SDVPN method)</a>
</li>
      <li><a href="atomman.Atoms.html#atomman.Atoms.model">model() (atomman.Atoms method)</a>

      <ul>
        <li><a href="atomman.Box.html#atomman.Box.model">(atomman.Box method)</a>
</li>
        <li><a href="atomman.cluster.BondAngleMap.html#atomman.cluster.BondAngleMap.model">(atomman.cluster.BondAngleMap method)</a>
</li>
        <li><a href="atomman.defect.GammaSurface.html#atomman.defect.GammaSurface.model">(atomman.defect.GammaSurface method)</a>
</li>
        <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.model">(atomman.defect.SDVPN method)</a>
</li>
        <li><a href="atomman.ElasticConstants.html#atomman.ElasticConstants.model">(atomman.ElasticConstants method)</a>
</li>
        <li><a href="atomman.System.html#atomman.System.model">(atomman.System method)</a>
</li>
        <li><a href="atomman.unitconvert.html#atomman.unitconvert.model">(in module atomman.unitconvert)</a>
</li>
      </ul></li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.library.record.CrystalPrototype.html#atomman.library.record.CrystalPrototype.modelroot">modelroot() (atomman.library.record.CrystalPrototype property)</a>

      <ul>
        <li><a href="atomman.library.record.ReferenceCrystal.html#atomman.library.record.ReferenceCrystal.modelroot">(atomman.library.record.ReferenceCrystal property)</a>
</li>
        <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.modelroot">(atomman.library.record.RelaxedCrystal property)</a>
</li>
      </ul></li>
      <li><a href="atomman.library.record.CrystalPrototype.html#atomman.library.record.CrystalPrototype.mongoquery">mongoquery() (atomman.library.record.CrystalPrototype static method)</a>

      <ul>
        <li><a href="atomman.library.record.ReferenceCrystal.html#atomman.library.record.ReferenceCrystal.mongoquery">(atomman.library.record.ReferenceCrystal static method)</a>
</li>
        <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.mongoquery">(atomman.library.record.RelaxedCrystal static method)</a>
</li>
      </ul></li>
      <li><a href="atomman.Box.html#atomman.Box.monoclinic">monoclinic() (atomman.Box class method)</a>

      <ul>
        <li><a href="atomman.ElasticConstants.html#atomman.ElasticConstants.monoclinic">(atomman.ElasticConstants method)</a>
</li>
      </ul></li>
      <li><a href="atomman.defect.Dislocation.html#atomman.defect.Dislocation.monopole">monopole() (atomman.defect.Dislocation method)</a>
</li>
      <li><a href="atomman.defect.IsotropicVolterraDislocation.html#atomman.defect.IsotropicVolterraDislocation.mu">mu() (atomman.defect.IsotropicVolterraDislocation property)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="N">N</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.defect.VolterraDislocation.html#atomman.defect.VolterraDislocation.n">n() (atomman.defect.VolterraDislocation property)</a>
</li>
      <li><a href="atomman.Atoms.html#atomman.Atoms.natoms">natoms() (atomman.Atoms property)</a>

      <ul>
        <li><a href="atomman.library.record.ReferenceCrystal.html#atomman.library.record.ReferenceCrystal.natoms">(atomman.library.record.ReferenceCrystal property)</a>
</li>
        <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.natoms">(atomman.library.record.RelaxedCrystal property)</a>
</li>
        <li><a href="atomman.System.html#atomman.System.natoms">(atomman.System property)</a>
</li>
      </ul></li>
      <li><a href="atomman.Atoms.html#atomman.Atoms.natypes">natypes() (atomman.Atoms property)</a>

      <ul>
        <li><a href="atomman.library.record.CrystalPrototype.html#atomman.library.record.CrystalPrototype.natypes">(atomman.library.record.CrystalPrototype property)</a>
</li>
        <li><a href="atomman.library.record.ReferenceCrystal.html#atomman.library.record.ReferenceCrystal.natypes">(atomman.library.record.ReferenceCrystal property)</a>
</li>
        <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.natypes">(atomman.library.record.RelaxedCrystal property)</a>
</li>
        <li><a href="atomman.System.html#atomman.System.natypes">(atomman.System property)</a>
</li>
      </ul></li>
      <li><a href="atomman.lammps.NEBLog.html#atomman.lammps.NEBLog">NEBLog (class in atomman.lammps)</a>
</li>
      <li><a href="atomman.NeighborList.html#atomman.NeighborList">NeighborList (class in atomman)</a>
</li>
      <li><a href="atomman.System.html#atomman.System.neighborlist">neighborlist() (atomman.System method)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.defect.DifferentialDisplacement.html#atomman.defect.DifferentialDisplacement.neighbors">neighbors() (atomman.defect.DifferentialDisplacement property)</a>

      <ul>
        <li><a href="atomman.defect.Strain.html#atomman.defect.Strain.neighbors">(atomman.defect.Strain property)</a>
</li>
      </ul></li>
      <li><a href="atomman.NeighborList.html#atomman.NeighborList.nlist">nlist() (atomman.NeighborList property)</a>

      <ul>
        <li><a href="atomman.html#atomman.nlist">(in module atomman)</a>
</li>
      </ul></li>
      <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.nonlocal_energy">nonlocal_energy() (atomman.defect.SDVPN method)</a>
</li>
      <li><a href="atomman.region.html#atomman.region.Plane.normal">normal() (atomman.region.Plane property)</a>
</li>
      <li><a href="atomman.System.html#atomman.System.normalize">normalize() (atomman.System method)</a>

      <ul>
        <li><a href="atomman.lammps.html#atomman.lammps.normalize">(in module atomman.lammps)</a>
</li>
      </ul></li>
      <li><a href="atomman.ElasticConstants.html#atomman.ElasticConstants.normalized_as">normalized_as() (atomman.ElasticConstants method)</a>
</li>
      <li><a href="atomman.lammps.NEBLog.html#atomman.lammps.NEBLog.nreplicas">nreplicas() (atomman.lammps.NEBLog property)</a>
</li>
      <li><a href="atomman.defect.IsotropicVolterraDislocation.html#atomman.defect.IsotropicVolterraDislocation.nu">nu() (atomman.defect.IsotropicVolterraDislocation property)</a>
</li>
      <li><a href="atomman.defect.Strain.html#atomman.defect.Strain.nye">nye() (atomman.defect.Strain property)</a>
</li>
      <li><a href="atomman.defect.html#atomman.defect.nye_tensor">nye_tensor() (in module atomman.defect)</a>
</li>
      <li><a href="atomman.defect.html#atomman.defect.nye_tensor_p">nye_tensor_p() (in module atomman.defect)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="O">O</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.Box.html#atomman.Box.origin">origin() (atomman.Box property)</a>
</li>
      <li><a href="atomman.Box.html#atomman.Box.orthorhombic">orthorhombic() (atomman.Box class method)</a>

      <ul>
        <li><a href="atomman.ElasticConstants.html#atomman.ElasticConstants.orthorhombic">(atomman.ElasticConstants method)</a>
</li>
      </ul></li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.region.html#atomman.region.Shape.outside">outside() (atomman.region.Shape method)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="P">P</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.defect.Stroh.html#atomman.defect.Stroh.p">p() (atomman.defect.Stroh property)</a>
</li>
      <li><a href="atomman.defect.Strain.html#atomman.defect.Strain.p_vectors">p_vectors() (atomman.defect.Strain property)</a>
</li>
      <li><a href="atomman.library.record.CrystalPrototype.html#atomman.library.record.CrystalPrototype.pandasfilter">pandasfilter() (atomman.library.record.CrystalPrototype static method)</a>

      <ul>
        <li><a href="atomman.library.record.ReferenceCrystal.html#atomman.library.record.ReferenceCrystal.pandasfilter">(atomman.library.record.ReferenceCrystal static method)</a>
</li>
        <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.pandasfilter">(atomman.library.record.RelaxedCrystal static method)</a>
</li>
      </ul></li>
      <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.parent_key">parent_key() (atomman.library.record.RelaxedCrystal property)</a>
</li>
      <li><a href="atomman.unitconvert.html#atomman.unitconvert.parse">parse() (in module atomman.unitconvert)</a>
</li>
      <li><a href="atomman.defect.GammaSurface.html#atomman.defect.GammaSurface.path">path() (atomman.defect.GammaSurface method)</a>
</li>
      <li><a href="atomman.System.html#atomman.System.pbc">pbc() (atomman.System property)</a>
</li>
      <li><a href="atomman.cluster.BondAngleMap.html#atomman.cluster.BondAngleMap.pdf">pdf() (atomman.cluster.BondAngleMap method)</a>
</li>
      <li><a href="atomman.library.record.CrystalPrototype.html#atomman.library.record.CrystalPrototype.pearson">pearson() (atomman.library.record.CrystalPrototype property)</a>
</li>
      <li><a href="atomman.defect.Dislocation.html#atomman.defect.Dislocation.periodicarray">periodicarray() (atomman.defect.Dislocation method)</a>
</li>
      <li><a href="atomman.region.html#atomman.region.Plane">Plane (class in atomman.region)</a>
</li>
      <li><a href="atomman.tools.html#atomman.tools.miller.plane3to4">plane3to4() (in module atomman.tools.miller)</a>
</li>
      <li><a href="atomman.tools.html#atomman.tools.miller.plane4to3">plane4to3() (in module atomman.tools.miller)</a>
</li>
      <li><a href="atomman.tools.html#atomman.tools.miller.plane_crystal_to_cartesian">plane_crystal_to_cartesian() (in module atomman.tools.miller)</a>
</li>
      <li><a href="atomman.defect.GammaSurface.html#atomman.defect.GammaSurface.planenormal">planenormal() (atomman.defect.GammaSurface property)</a>
</li>
      <li><a href="atomman.Box.html#atomman.Box.planes">planes() (atomman.Box property)</a>

      <ul>
        <li><a href="atomman.region.html#atomman.region.PlaneSet.planes">(atomman.region.PlaneSet property)</a>
</li>
      </ul></li>
      <li><a href="atomman.region.html#atomman.region.PlaneSet">PlaneSet (class in atomman.region)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.defect.DifferentialDisplacement.html#atomman.defect.DifferentialDisplacement.plot">plot() (atomman.defect.DifferentialDisplacement method)</a>
</li>
      <li><a href="atomman.cluster.BondAngleMap.html#atomman.cluster.BondAngleMap.plot_cumulative_pdf">plot_cumulative_pdf() (atomman.cluster.BondAngleMap method)</a>
</li>
      <li><a href="atomman.mep.BasePath.html#atomman.mep.BasePath.plot_energy">plot_energy() (atomman.mep.BasePath method)</a>
</li>
      <li><a href="atomman.mep.BasePath.html#atomman.mep.BasePath.plot_force">plot_force() (atomman.mep.BasePath method)</a>
</li>
      <li><a href="atomman.cluster.BondAngleMap.html#atomman.cluster.BondAngleMap.plot_pdf">plot_pdf() (atomman.cluster.BondAngleMap method)</a>
</li>
      <li><a href="atomman.defect.html#atomman.defect.pn_arctan_disregistry">pn_arctan_disregistry() (in module atomman.defect)</a>
</li>
      <li><a href="atomman.region.html#atomman.region.Plane.point">point() (atomman.region.Plane property)</a>

      <ul>
        <li><a href="atomman.defect.html#atomman.defect.point">(in module atomman.defect)</a>
</li>
      </ul></li>
      <li><a href="atomman.defect.GammaSurface.html#atomman.defect.GammaSurface.pos_to_a12">pos_to_a12() (atomman.defect.GammaSurface method)</a>
</li>
      <li><a href="atomman.defect.GammaSurface.html#atomman.defect.GammaSurface.pos_to_xy">pos_to_xy() (atomman.defect.GammaSurface method)</a>
</li>
      <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.potential_energy">potential_energy() (atomman.library.record.RelaxedCrystal property)</a>
</li>
      <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.potential_id">potential_id() (atomman.library.record.RelaxedCrystal property)</a>
</li>
      <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.potential_key">potential_key() (atomman.library.record.RelaxedCrystal property)</a>
</li>
      <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.potential_LAMMPS_id">potential_LAMMPS_id() (atomman.library.record.RelaxedCrystal property)</a>
</li>
      <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.potential_LAMMPS_key">potential_LAMMPS_key() (atomman.library.record.RelaxedCrystal property)</a>
</li>
      <li><a href="atomman.defect.Stroh.html#atomman.defect.Stroh.preln">preln() (atomman.defect.Stroh property)</a>

      <ul>
        <li><a href="atomman.defect.VolterraDislocation.html#atomman.defect.VolterraDislocation.preln">(atomman.defect.VolterraDislocation property)</a>
</li>
      </ul></li>
      <li><a href="atomman.Atoms.html#atomman.Atoms.prop">prop() (atomman.Atoms method)</a>
</li>
      <li><a href="atomman.Atoms.html#atomman.Atoms.prop_atype">prop_atype() (atomman.Atoms method)</a>
</li>
      <li><a href="atomman.library.record.CrystalPrototype.html#atomman.library.record.CrystalPrototype.prototype">prototype() (atomman.library.record.CrystalPrototype property)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="R">R</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.System.html#atomman.System.r0">r0() (atomman.System method)</a>
</li>
      <li><a href="atomman.region.html#atomman.region.Cylinder.radius">radius() (atomman.region.Cylinder property)</a>

      <ul>
        <li><a href="atomman.region.html#atomman.region.Sphere.radius">(atomman.region.Sphere property)</a>
</li>
      </ul></li>
      <li><a href="atomman.defect.Dislocation.html#atomman.defect.Dislocation.rcell">rcell() (atomman.defect.Dislocation property)</a>

      <ul>
        <li><a href="atomman.defect.FreeSurface.html#atomman.defect.FreeSurface.rcell">(atomman.defect.FreeSurface property)</a>
</li>
      </ul></li>
      <li><a href="atomman.defect.FreeSurface.html#atomman.defect.FreeSurface.rcellwidth">rcellwidth() (atomman.defect.FreeSurface property)</a>
</li>
      <li><a href="atomman.lammps.Log.html#atomman.lammps.Log.read">read() (atomman.lammps.Log method)</a>
</li>
      <li><a href="atomman.defect.DifferentialDisplacement.html#atomman.defect.DifferentialDisplacement.reference">reference() (atomman.defect.DifferentialDisplacement property)</a>
</li>
      <li><a href="atomman.library.record.ReferenceCrystal.html#atomman.library.record.ReferenceCrystal">ReferenceCrystal (class in atomman.library.record)</a>
</li>
      <li><a href="atomman.mep.BasePath.html#atomman.mep.BasePath.relax">relax() (atomman.mep.BasePath method)</a>

      <ul>
        <li><a href="atomman.mep.ISMPath.html#atomman.mep.ISMPath.relax">(atomman.mep.ISMPath method)</a>
</li>
      </ul></li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal">RelaxedCrystal (class in atomman.library.record)</a>
</li>
      <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.res">res() (atomman.defect.SDVPN property)</a>
</li>
      <li><a href="atomman.unitconvert.html#atomman.unitconvert.reset_units">reset_units() (in module atomman.unitconvert)</a>
</li>
      <li><a href="atomman.ElasticConstants.html#atomman.ElasticConstants.rhombohedral">rhombohedral() (atomman.ElasticConstants method)</a>
</li>
      <li><a href="atomman.cluster.BondAngleMap.html#atomman.cluster.BondAngleMap.rmax">rmax() (atomman.cluster.BondAngleMap property)</a>
</li>
      <li><a href="atomman.cluster.BondAngleMap.html#atomman.cluster.BondAngleMap.rmin">rmin() (atomman.cluster.BondAngleMap property)</a>
</li>
      <li><a href="atomman.cluster.BondAngleMap.html#atomman.cluster.BondAngleMap.rnum">rnum() (atomman.cluster.BondAngleMap property)</a>
</li>
      <li><a href="atomman.System.html#atomman.System.rotate">rotate() (atomman.System method)</a>
</li>
      <li><a href="atomman.defect.Strain.html#atomman.defect.Strain.rotation">rotation() (atomman.defect.Strain property)</a>
</li>
      <li><a href="atomman.lammps.html#atomman.lammps.run">run() (in module atomman.lammps)</a>
</li>
      <li><a href="atomman.mep.html#atomman.mep.integrator.rungekutta">rungekutta() (in module atomman.mep.integrator)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="S">S</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.cluster.BondAngleMap.html#atomman.cluster.BondAngleMap.save_table">save_table() (atomman.cluster.BondAngleMap method)</a>
</li>
      <li><a href="atomman.defect.Strain.html#atomman.defect.Strain.save_to_system">save_to_system (atomman.defect.Strain attribute)</a>
</li>
      <li><a href="atomman.System.html#atomman.System.scale">scale() (atomman.System method)</a>
</li>
      <li><a href="atomman.tools.html#atomman.tools.screen_input">screen_input() (in module atomman.tools)</a>
</li>
      <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN">SDVPN (class in atomman.defect)</a>
</li>
      <li><a href="atomman.Box.html#atomman.Box.set">set() (atomman.Box method)</a>

      <ul>
        <li><a href="atomman.cluster.BondAngleMap.html#atomman.cluster.BondAngleMap.set">(atomman.cluster.BondAngleMap method)</a>
</li>
        <li><a href="atomman.defect.GammaSurface.html#atomman.defect.GammaSurface.set">(atomman.defect.GammaSurface method)</a>
</li>
      </ul></li>
      <li><a href="atomman.Box.html#atomman.Box.set_abc">set_abc() (atomman.Box method)</a>
</li>
      <li><a href="atomman.Box.html#atomman.Box.set_hi_los">set_hi_los() (atomman.Box method)</a>
</li>
      <li><a href="atomman.unitconvert.html#atomman.unitconvert.set_in_units">set_in_units() (in module atomman.unitconvert)</a>
</li>
      <li><a href="atomman.Box.html#atomman.Box.set_lengths">set_lengths() (atomman.Box method)</a>
</li>
      <li><a href="atomman.unitconvert.html#atomman.unitconvert.set_literal">set_literal() (in module atomman.unitconvert)</a>
</li>
      <li><a href="atomman.defect.Strain.html#atomman.defect.Strain.set_p_vectors">set_p_vectors (atomman.defect.Strain attribute)</a>
</li>
      <li><a href="atomman.library.record.ReferenceCrystal.html#atomman.library.record.ReferenceCrystal.set_values">set_values() (atomman.library.record.ReferenceCrystal method)</a>
</li>
      <li><a href="atomman.Box.html#atomman.Box.set_vectors">set_vectors() (atomman.Box method)</a>
</li>
      <li><a href="atomman.library.record.CrystalPrototype.html#atomman.library.record.CrystalPrototype.sg_hm">sg_hm() (atomman.library.record.CrystalPrototype property)</a>
</li>
      <li><a href="atomman.library.record.CrystalPrototype.html#atomman.library.record.CrystalPrototype.sg_number">sg_number() (atomman.library.record.CrystalPrototype property)</a>
</li>
      <li><a href="atomman.library.record.CrystalPrototype.html#atomman.library.record.CrystalPrototype.sg_schoenflies">sg_schoenflies() (atomman.library.record.CrystalPrototype property)</a>
</li>
      <li><a href="atomman.region.html#atomman.region.Shape">Shape (class in atomman.region)</a>
</li>
      <li><a href="atomman.ElasticConstants.html#atomman.ElasticConstants.shear">shear() (atomman.ElasticConstants method)</a>
</li>
      <li><a href="atomman.defect.Dislocation.html#atomman.defect.Dislocation.shift">shift() (atomman.defect.Dislocation property)</a>
</li>
      <li><a href="atomman.defect.Dislocation.html#atomman.defect.Dislocation.shifts">shifts() (atomman.defect.Dislocation property)</a>

      <ul>
        <li><a href="atomman.defect.FreeSurface.html#atomman.defect.FreeSurface.shifts">(atomman.defect.FreeSurface property)</a>
</li>
      </ul></li>
      <li><a href="atomman.ElasticConstants.html#atomman.ElasticConstants.Sij">Sij() (atomman.ElasticConstants property)</a>
</li>
      <li><a href="atomman.ElasticConstants.html#atomman.ElasticConstants.Sijkl">Sijkl() (atomman.ElasticConstants property)</a>
</li>
      <li><a href="atomman.lammps.Log.html#atomman.lammps.Log.simulations">simulations() (atomman.lammps.Log property)</a>
</li>
      <li><a href="atomman.defect.html#atomman.defect.slip_vector">slip_vector() (in module atomman.defect)</a>
</li>
      <li><a href="atomman.defect.DifferentialDisplacement.html#atomman.defect.DifferentialDisplacement.solve">solve() (atomman.defect.DifferentialDisplacement method)</a>

      <ul>
        <li><a href="atomman.defect.IsotropicVolterraDislocation.html#atomman.defect.IsotropicVolterraDislocation.solve">(atomman.defect.IsotropicVolterraDislocation method)</a>
</li>
        <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.solve">(atomman.defect.SDVPN method)</a>
</li>
        <li><a href="atomman.defect.Stroh.html#atomman.defect.Stroh.solve">(atomman.defect.Stroh method)</a>
</li>
        <li><a href="atomman.defect.VolterraDislocation.html#atomman.defect.VolterraDislocation.solve">(atomman.defect.VolterraDislocation method)</a>
</li>
      </ul></li>
      <li><a href="atomman.defect.Strain.html#atomman.defect.Strain.solve_G">solve_G (atomman.defect.Strain attribute)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.defect.Strain.html#atomman.defect.Strain.solve_nye">solve_nye (atomman.defect.Strain attribute)</a>
</li>
      <li><a href="atomman.defect.html#atomman.defect.solve_volterra_dislocation">solve_volterra_dislocation() (in module atomman.defect)</a>
</li>
      <li><a href="atomman.library.record.ReferenceCrystal.html#atomman.library.record.ReferenceCrystal.sourcelink">sourcelink() (atomman.library.record.ReferenceCrystal property)</a>
</li>
      <li><a href="atomman.library.record.ReferenceCrystal.html#atomman.library.record.ReferenceCrystal.sourcename">sourcename() (atomman.library.record.ReferenceCrystal property)</a>
</li>
      <li><a href="atomman.region.html#atomman.region.Sphere">Sphere (class in atomman.region)</a>
</li>
      <li><a href="atomman.defect.StackingFault.html#atomman.defect.StackingFault">StackingFault (class in atomman.defect)</a>
</li>
      <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.standing">standing() (atomman.library.record.RelaxedCrystal property)</a>
</li>
      <li><a href="atomman.mep.BasePath.html#atomman.mep.BasePath.step">step() (atomman.mep.BasePath method)</a>

      <ul>
        <li><a href="atomman.mep.ISMPath.html#atomman.mep.ISMPath.step">(atomman.mep.ISMPath method)</a>
</li>
      </ul></li>
      <li><a href="atomman.defect.Strain.html#atomman.defect.Strain">Strain (class in atomman.defect)</a>
</li>
      <li><a href="atomman.defect.Strain.html#atomman.defect.Strain.strain">strain() (atomman.defect.Strain property)</a>
</li>
      <li><a href="atomman.defect.IsotropicVolterraDislocation.html#atomman.defect.IsotropicVolterraDislocation.stress">stress() (atomman.defect.IsotropicVolterraDislocation method)</a>

      <ul>
        <li><a href="atomman.defect.Stroh.html#atomman.defect.Stroh.stress">(atomman.defect.Stroh method)</a>
</li>
        <li><a href="atomman.defect.VolterraDislocation.html#atomman.defect.VolterraDislocation.stress">(atomman.defect.VolterraDislocation method)</a>
</li>
      </ul></li>
      <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.stress_energy">stress_energy() (atomman.defect.SDVPN method)</a>
</li>
      <li><a href="atomman.defect.Stroh.html#atomman.defect.Stroh">Stroh (class in atomman.defect)</a>
</li>
      <li><a href="atomman.library.record.CrystalPrototype.html#atomman.library.record.CrystalPrototype.strukturbericht">strukturbericht() (atomman.library.record.CrystalPrototype property)</a>
</li>
      <li><a href="atomman.library.record.CrystalPrototype.html#atomman.library.record.CrystalPrototype.style">style() (atomman.library.record.CrystalPrototype property)</a>

      <ul>
        <li><a href="atomman.library.record.ReferenceCrystal.html#atomman.library.record.ReferenceCrystal.style">(atomman.library.record.ReferenceCrystal property)</a>
</li>
        <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.style">(atomman.library.record.RelaxedCrystal property)</a>
</li>
      </ul></li>
      <li><a href="atomman.defect.html#atomman.defect.substitutional">substitutional() (in module atomman.defect)</a>
</li>
      <li><a href="atomman.System.html#atomman.System.supersize">supersize() (atomman.System method)</a>
</li>
      <li><a href="atomman.defect.FreeSurface.html#atomman.defect.FreeSurface.surface">surface() (atomman.defect.FreeSurface method)</a>

      <ul>
        <li><a href="atomman.defect.StackingFault.html#atomman.defect.StackingFault.surface">(atomman.defect.StackingFault method)</a>
</li>
      </ul></li>
      <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.surface_energy">surface_energy() (atomman.defect.SDVPN method)</a>
</li>
      <li><a href="atomman.defect.FreeSurface.html#atomman.defect.FreeSurface.surfacearea">surfacearea() (atomman.defect.FreeSurface property)</a>
</li>
      <li><a href="atomman.cluster.BondAngleMap.html#atomman.cluster.BondAngleMap.symbols">symbols() (atomman.cluster.BondAngleMap property)</a>

      <ul>
        <li><a href="atomman.library.record.ReferenceCrystal.html#atomman.library.record.ReferenceCrystal.symbols">(atomman.library.record.ReferenceCrystal property)</a>
</li>
        <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.symbols">(atomman.library.record.RelaxedCrystal property)</a>
</li>
        <li><a href="atomman.System.html#atomman.System.symbols">(atomman.System property)</a>
</li>
      </ul></li>
      <li><a href="atomman.System.html#atomman.System">System (class in atomman)</a>
</li>
      <li><a href="atomman.defect.FreeSurface.html#atomman.defect.FreeSurface.system">system() (atomman.defect.FreeSurface property)</a>

      <ul>
        <li><a href="atomman.defect.Strain.html#atomman.defect.Strain.system">(atomman.defect.Strain property)</a>
</li>
      </ul></li>
      <li><a href="atomman.defect.DifferentialDisplacement.html#atomman.defect.DifferentialDisplacement.system0">system0() (atomman.defect.DifferentialDisplacement property)</a>
</li>
      <li><a href="atomman.defect.DifferentialDisplacement.html#atomman.defect.DifferentialDisplacement.system1">system1() (atomman.defect.DifferentialDisplacement property)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="T">T</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.tau">tau() (atomman.defect.SDVPN property)</a>
</li>
      <li><a href="atomman.Box.html#atomman.Box.tetragonal">tetragonal() (atomman.Box class method)</a>

      <ul>
        <li><a href="atomman.ElasticConstants.html#atomman.ElasticConstants.tetragonal">(atomman.ElasticConstants method)</a>
</li>
      </ul></li>
      <li><a href="atomman.defect.IsotropicVolterraDislocation.html#atomman.defect.IsotropicVolterraDislocation.theta">theta() (atomman.defect.IsotropicVolterraDislocation method)</a>
</li>
      <li><a href="atomman.defect.Strain.html#atomman.defect.Strain.theta_max">theta_max() (atomman.defect.Strain property)</a>
</li>
      <li><a href="atomman.cluster.BondAngleMap.html#atomman.cluster.BondAngleMap.thetamax">thetamax() (atomman.cluster.BondAngleMap property)</a>
</li>
      <li><a href="atomman.cluster.BondAngleMap.html#atomman.cluster.BondAngleMap.thetamin">thetamin() (atomman.cluster.BondAngleMap property)</a>
</li>
      <li><a href="atomman.cluster.BondAngleMap.html#atomman.cluster.BondAngleMap.thetanum">thetanum() (atomman.cluster.BondAngleMap property)</a>
</li>
      <li><a href="atomman.lammps.html#atomman.lammps.style.timestep">timestep() (in module atomman.lammps.style)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.defect.VolterraDislocation.html#atomman.defect.VolterraDislocation.tol">tol() (atomman.defect.VolterraDislocation property)</a>
</li>
      <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.total_energy">total_energy() (atomman.defect.SDVPN method)</a>
</li>
      <li><a href="atomman.defect.Dislocation.html#atomman.defect.Dislocation.transform">transform() (atomman.defect.Dislocation property)</a>

      <ul>
        <li><a href="atomman.defect.FreeSurface.html#atomman.defect.FreeSurface.transform">(atomman.defect.FreeSurface property)</a>
</li>
        <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.transform">(atomman.defect.SDVPN property)</a>
</li>
        <li><a href="atomman.defect.VolterraDislocation.html#atomman.defect.VolterraDislocation.transform">(atomman.defect.VolterraDislocation property)</a>
</li>
        <li><a href="atomman.ElasticConstants.html#atomman.ElasticConstants.transform">(atomman.ElasticConstants method)</a>
</li>
      </ul></li>
      <li><a href="atomman.Box.html#atomman.Box.triclinic">triclinic() (atomman.Box class method)</a>

      <ul>
        <li><a href="atomman.ElasticConstants.html#atomman.ElasticConstants.triclinic">(atomman.ElasticConstants method)</a>
</li>
      </ul></li>
      <li><a href="atomman.Box.html#atomman.Box.trigonal">trigonal() (atomman.Box class method)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="U">U</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.tools.html#atomman.tools.uber_open_rmode">uber_open_rmode (class in atomman.tools)</a>
</li>
      <li><a href="atomman.defect.Dislocation.html#atomman.defect.Dislocation.ucell">ucell() (atomman.defect.Dislocation property)</a>

      <ul>
        <li><a href="atomman.defect.FreeSurface.html#atomman.defect.FreeSurface.ucell">(atomman.defect.FreeSurface property)</a>
</li>
        <li><a href="atomman.library.record.CrystalPrototype.html#atomman.library.record.CrystalPrototype.ucell">(atomman.library.record.CrystalPrototype property)</a>
</li>
        <li><a href="atomman.library.record.ReferenceCrystal.html#atomman.library.record.ReferenceCrystal.ucell">(atomman.library.record.ReferenceCrystal property)</a>
</li>
        <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.ucell">(atomman.library.record.RelaxedCrystal property)</a>
</li>
      </ul></li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.lammps.html#atomman.lammps.style.unit">unit() (in module atomman.lammps.style)</a>
</li>
      <li><a href="atomman.mep.BasePath.html#atomman.mep.BasePath.unittangent">unittangent() (atomman.mep.BasePath property)</a>

      <ul>
        <li><a href="atomman.mep.ISMPath.html#atomman.mep.ISMPath.unittangent">(atomman.mep.ISMPath property)</a>
</li>
      </ul></li>
      <li><a href="atomman.System.html#atomman.System.unscale">unscale() (atomman.System method)</a>
</li>
      <li><a href="atomman.defect.Dislocation.html#atomman.defect.Dislocation.uvws">uvws() (atomman.defect.Dislocation property)</a>

      <ul>
        <li><a href="atomman.defect.FreeSurface.html#atomman.defect.FreeSurface.uvws">(atomman.defect.FreeSurface property)</a>
</li>
      </ul></li>
  </ul></td>
</tr></table>

<h2 id="V">V</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.defect.html#atomman.defect.vacancy">vacancy() (in module atomman.defect)</a>
</li>
      <li><a href="atomman.unitconvert.html#atomman.unitconvert.value_unit">value_unit() (in module atomman.unitconvert)</a>
</li>
      <li><a href="atomman.tools.html#atomman.tools.vect_angle">vect_angle() (in module atomman.tools)</a>
</li>
      <li><a href="atomman.tools.html#atomman.tools.miller.vector3to4">vector3to4() (in module atomman.tools.miller)</a>
</li>
      <li><a href="atomman.tools.html#atomman.tools.miller.vector4to3">vector4to3() (in module atomman.tools.miller)</a>
</li>
      <li><a href="atomman.tools.html#atomman.tools.miller.vector_conventional_to_primitive">vector_conventional_to_primitive() (in module atomman.tools.miller)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.tools.html#atomman.tools.miller.vector_crystal_to_cartesian">vector_crystal_to_cartesian() (in module atomman.tools.miller)</a>
</li>
      <li><a href="atomman.tools.html#atomman.tools.miller.vector_primitive_to_conventional">vector_primitive_to_conventional() (in module atomman.tools.miller)</a>
</li>
      <li><a href="atomman.Box.html#atomman.Box.vects">vects() (atomman.Box property)</a>
</li>
      <li><a href="atomman.Atoms.html#atomman.Atoms.view">view() (atomman.Atoms property)</a>
</li>
      <li><a href="atomman.defect.VolterraDislocation.html#atomman.defect.VolterraDislocation">VolterraDislocation (class in atomman.defect)</a>
</li>
      <li><a href="atomman.Box.html#atomman.Box.volume">volume() (atomman.Box property)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="W">W</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.System.html#atomman.System.wrap">wrap() (atomman.System method)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="X">X</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.defect.SDVPN.html#atomman.defect.SDVPN.x">x() (atomman.defect.SDVPN property)</a>
</li>
      <li><a href="atomman.Box.html#atomman.Box.xhi">xhi() (atomman.Box property)</a>
</li>
      <li><a href="atomman.Box.html#atomman.Box.xlo">xlo() (atomman.Box property)</a>
</li>
      <li><a href="atomman.library.record.CrystalPrototype.html#atomman.library.record.CrystalPrototype.xsd_filename">xsd_filename() (atomman.library.record.CrystalPrototype property)</a>

      <ul>
        <li><a href="atomman.library.record.ReferenceCrystal.html#atomman.library.record.ReferenceCrystal.xsd_filename">(atomman.library.record.ReferenceCrystal property)</a>
</li>
        <li><a href="atomman.library.record.RelaxedCrystal.html#atomman.library.record.RelaxedCrystal.xsd_filename">(atomman.library.record.RelaxedCrystal property)</a>
</li>
      </ul></li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.Box.html#atomman.Box.xy">xy() (atomman.Box property)</a>
</li>
      <li><a href="atomman.defect.GammaSurface.html#atomman.defect.GammaSurface.xy_to_a12">xy_to_a12() (atomman.defect.GammaSurface method)</a>
</li>
      <li><a href="atomman.defect.GammaSurface.html#atomman.defect.GammaSurface.xy_to_pos">xy_to_pos() (atomman.defect.GammaSurface method)</a>
</li>
      <li><a href="atomman.Box.html#atomman.Box.xz">xz() (atomman.Box property)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="Y">Y</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.Box.html#atomman.Box.yhi">yhi() (atomman.Box property)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.Box.html#atomman.Box.ylo">ylo() (atomman.Box property)</a>
</li>
      <li><a href="atomman.Box.html#atomman.Box.yz">yz() (atomman.Box property)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="Z">Z</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.Box.html#atomman.Box.zhi">zhi() (atomman.Box property)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.Box.html#atomman.Box.zlo">zlo() (atomman.Box property)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="Ξ">Ξ</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomman.defect.VolterraDislocation.html#atomman.defect.VolterraDislocation.ξ">ξ() (atomman.defect.VolterraDislocation property)</a>
</li>
  </ul></td>
</tr></table>



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